We just carry our LO through the metal detector. I wouldn't ever walk through or take my LO through those Xray machines..
If you don't want to watch through the metal detector I'm sure you can ask for a pat down.
Where you flying?

@Andrea: Last time I flew I saw some little kids go through the full body scanner - the youngest was maybe 5? Unfortunately I think it is required for everyone who is "assigned" to the scanner. At my airport, some people are routed through to a regular metal detector and some to the scanner, and it's luck of the draw, so maybe you won't have to? If you do, I would just say you want to opt out and get the pat down. I go through the scanner now and it's not a big deal to me, but if I was pregnant or had a LO, I would be very apprehensive too.

I just flew on Friday (I'm 32 weeks) and was able to decline the full body scanner and just do a standard metal detector with zero problems. The airport I flew through (Columbus OH) had signs everywhere telling you you could decline.